Highly ordered pyrolytic graphite (HOPG) surfaces were modified by the adsorption of Pd molecular precursors from solution. Two palladium-containing molecular precursors were studied, a mononuclear one and a trinuclear one, to compare their affinities and distributions at substrate surfaces. To obtain Pd nanoparticles, these neutral molecular precursors were reduced under a hydrogen atmosphere. Thermogravimetric analysis was carried out to establish the behavior of these precursors at various temperatures. Understanding the thermal stability of these compounds is very important to establish the appropriate conditions to form metallic Pd. The modified surface has been characterized by X-ray photoelectron spectroscopy (XPS) and atomic force microscopy; also, the reductive process was monitored by XPS. Remarkable differences were observed between the mononuclear and trinuclear compounds in terms of dispersion, particle size, and homogeneity. The preference of the trinuclear compound was to deposit at HOPG defects, in contrast to that of the mononuclear one, which was agglomeration on all surfaces. After the application of this technique, not only Pd nanoparticles but also Pd nanowires were obtained.